Thank you, Ralf and Nick for your help. I could see from the lof file that phenix.refine determined 2 sites at special positions, but I thought it did nothing about it, as the occupancies were brought back to 1. Thank you for your explanation that phenix.refine actually takes this into account. Maia Ralf W. Grosse-Kunstleve wrote:
Hi Maia,
I have a Ca2+ ion in a special position. the ocupancy should be 0.5, as the other half belongs to a symmetry-related molecule. However, refinement makes the occupansy 1. What should I do to prevent this? Should not it find automatically that?
phenix.refine uses the correct symmetry factor automatically (internally). Unless you have an actual partial occupancy, the occupancy factor in the pdb file should be 1, irrespective of the multiplicity of the special position.
Let me know if this doesn't answer your question.
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